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Evidence for a genetic component in ME/CFS - discussion thread

Discussion in 'BioMedical ME/CFS Research' started by Michiel Tack, Jul 30, 2020.

  1. Michiel Tack

    Michiel Tack Senior Member (Voting Rights)

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    I'm looking for evidence for a genetic component in ME/CFS and a discussion of the quality of evidence for each the studies.

    Here are some I found after a quick search (haven't read them all), are there important ones missing?

    Hickie et al. 2001. A Twin Study of the Etiology of Prolonged Fatigue and Immune Activation. https://www.cambridge.org/core/jour...e-activation/23C27BC6F37EC4D87ED788A9C0EB624C

    Buchwald et al. 2001. A twin study of chronic fatigue. https://journals.lww.com/psychosoma...11000/A_Twin_Study_of_Chronic_Fatigue.12.aspx

    Walsh et al. 2001. A family history study of chronic fatigue syndrome. https://journals.lww.com/psychgenet...tory_study_of_chronic_fatigue_syndrome.3.aspx

    Schur et al. 2007. Twin Analyses of Fatigue. https://www.cambridge.org/core/jour...s-of-fatigue/BEA61FF0469B1F6FA994D987478B68F2

    Ponting et al. 2018. Analysis of data from 500,000 individuals in UK Biobank demonstrates an inherited component to ME/CFS. https://mecfsresearchreview.me/2018...emonstrates-an-inherited-component-to-me-cfs/
     
  2. Trish

    Trish Moderator Staff Member

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    From forum threads:

    Autoimmunity-Related Risk Variants in PTPN22 and CTLA4 Are Associated With ME/CFS With Infectious Onset (2020) Scheibenbogen et al.
    Paper here Thread here

    In conclusion, our study shows that the PTPN22 rs2476601 and CTLA4 rs3087243 autoimmunity risk variants are more frequent in patients with ITO ME/CFS.
    But Chris Ponting checked and none of them showed up as risk factors in the UK Biobank and none of them showed up as CFS risk factors.

    Human Leukocyte Antigen alleles associated with ME/CFS: Fluge, Mella et al 2020
    We discovered two independent HLA associations, tagged by the alleles HLA-C*07:04 (OR 2.1 [95% CI 1.4–3.1]) and HLA-DQB1*03:03 (OR 1.5 [95% CI 1.1–2.0]). These alleles were carried by 7.7% and 12.7% of ME/CFS patients, respectively. The proportion of individuals carrying one or both of these alleles was 19.2% in the patient group and 12.2% in the control group (OR 1.7 [95% CI 1.3–2.2], pnc = 0.00003).
    Chris Ponting's comment: 'Small study, but great to see a genetic signal. This needs replication and more samples, but at the moment this does point towards an adaptive immune contribution to ME. Encouraging.'
    Paper here Thread here


    Genetic Predisposition for ME/CFS: A Pilot Study 2019 Perez Nathanson Klimas et al
    383 ME/CFS participants underwent DNA testing using the commercial company 23andMe.
    5693 SNPs were found to have at least 10% frequency in at least one cohort (ME/CFS or reference) and at least two-fold absolute difference for ME/CFS. Functional analysis identified the majority of SNPs as related to immune system, hormone, metabolic and extracellular matrix organization. CADD scoring identified 517 SNPs in these pathways that are among the 10% most deleteriousness substitutions to the human genome.
    Some suggestion on the thread of mistakes in the paper.
    Paper here Thread here
     
    Last edited: Jul 30, 2020
  3. Aslaug

    Aslaug Senior Member (Voting Rights)

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    Thanks for making a thread collecting all the different studies. I finally got around to annotating my genome data so I was thinking I'd look for SNPs that have shown up previously, but haven't had time to go looking for the studies. My lone data isn't worth a lot, but it's interesting for myself (and its the first time I've annotated a human genome, have only worked with bacteria genomes previously :rofl:)
     
  4. Jaybee00

    Jaybee00 Senior Member (Voting Rights)

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  5. wigglethemouse

    wigglethemouse Senior Member (Voting Rights)

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    This should have a good list:
    Review of the Quality Control Checks Performed by Current Genome-Wide and Targeted-Genome Association Studies on ME/CFS, 2020, Sepulveda et al
    Thread : https://www.s4me.info/threads/revie...studies-on-me-cfs-2020-sepulveda-et-al.15033/
    Paper : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7304330/

    Alan Light has a current R01 grant from NIH
    NOVEL GENE VARIANTS IN ME/CFS AND FIBROMYALGIA
    Grant : https://projectreporter.nih.gov/project_info_description.cfm?aid=9600713&icde=31258613
    Thread : Livestream Alan Light, PhD today at 6pm MST "New findings suggest that multiple mitochondrial mutations create susceptibility for ME/CFS"
    https://www.s4me.info/threads/lives...ations-create-susceptibility-for-me-cfs.7072/

    There are some HERV-K HERV-W studies as well. And quite a few gene expression studies.

    Please read the last two comments in that post from Paolo and Chris. It was ONE patient only that had the genetic variant that the blog talks about.
     
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  6. spinoza577

    spinoza577 Senior Member (Voting Rights)

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    Poeschla et al (incl. Buchwald) 2013 is as well about the Syndrome, as they say:
    Chronic Fatique and Personalitiy: A Twin Study of Causal Pathways and shared Liabilities
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3643988/

    page 6:
    ---
    Schlauch et al 2016: Genome wide analysis identifies genetic variations in [ME/CFS]
    https://www.nature.com/articles/tp2015208

    They found especially in non-coding regions some SNP´s being somehow common enough in ME/CFS, only 12 out of 442 in coding regions. This - the non-coding thing - may seem strange, but I have read something similar in respect of another diesease, sadly I have forgotten which one. In the introduction the highlight autism, schizophrenia and putative circadian clock. (I personally find the first two interesting as I think that the failure arises in the basal ganglia and non-specific thalamus, and at least schizophrenia should be located right there.)

    There is also the Perez/Klimas paper from 2019, but the data are said to be wrong.
     
  7. Jonathan Edwards

    Jonathan Edwards Senior Member (Voting Rights)

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    Simon and Chris Ponting refer to data by Canela-Xandri on BioRxiv. I could not track that down but Simon McGrath should know.

    I thought there was some recent information from a big epidemiological study in California that happened to check for CFS linkage. Again, Simon would know.
     
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  8. wigglethemouse

    wigglethemouse Senior Member (Voting Rights)

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    Perhaps you are thinking of the Lily Chu paper
    Onset Patterns and Course of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome
    https://www.frontiersin.org/articles/10.3389/fped.2019.00012/full

     
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  9. wigglethemouse

    wigglethemouse Senior Member (Voting Rights)

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    Paolo Maccallini referred to Canela-Xandri's paper where he looked at the supplementary data of that paper to locate that only ONE ME patient had the variant described in Simons blog about Chris Pontings analysis of interesting variants that @Michiel Tack lists in the first post. Oh boy, that was a mouthful.
     
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  10. wigglethemouse

    wigglethemouse Senior Member (Voting Rights)

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    I picked just one value from table 1 of that paper. rs41493945 has an allele frequency of ~0.3% with a variation of C->T. I double checked the coordinates given and it matches the rsID. They show the variant as G->A with a huge difference between patients and control which is not right. This must be a mistake.

    upload_2020-7-30_16-44-29.png upload_2020-7-30_16-38-25.png

    By the way, this is a GWAS with 42 patients and 38 controls. 20,000 ME and up to 500K controls will be a huge improvement with the DecodeME study.
     
  11. sea

    sea Senior Member (Voting Rights)

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    I’m not sure what you’re thinking is a mistake. Do you mean C>T being written as G>A? This most likely is not a mistake, but simply that one group is reporting using the forward strand (+) and the other using the reverse (-)
    When comparing your results you always have to look at which way it is being reported.
     
  12. wigglethemouse

    wigglethemouse Senior Member (Voting Rights)

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    I've no idea what you are talking about. The data in the table seems to be referenced to GRCh38 where the reference allele is T and the variant is C according to official databases. Take a look at the first three variants in table 1 - they all conform correctly and call out the right reference and alternate alleles so why doesn't rs41493945?

    Also 33 out of 42 CFS or 79% have the variant when the allele frequency is 0.3%. That's not right. That cannot happen. There are other examples in the table where the frequency is all wrong.

    Okay let me pick another one at random. rs16827966 has an allele frequency of ~3% but 30 out of 42 or 71% CFS have the variant but only 1 out of 38 or 2.6% controls. Controls are in the right range but CFS is not. The numbers are too far off. The reference allele is C and the alternate is T which they get correct this time.
    upload_2020-7-30_18-44-3.png
    upload_2020-7-30_18-48-1.png
    And they are sloppy. They leave the chromosome empty for this one when it should be 2.
     

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    Last edited: Jul 31, 2020
  13. wigglethemouse

    wigglethemouse Senior Member (Voting Rights)

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    Here is more evidence that the Schlauch et al 2016 paper is wrong. I searched for all the hugely significant variants in table 1 of that paper in the UK Biobank GWAS tool and selected data for chronic fatigue syndrome that has data for 2017 cases and 450247 controls, slighty more than Schlauch 42 CFS and 38 controls.

    http://geneatlas.roslin.ed.ac.uk/se...010471+rs6757577+rs8029503+rs7849492+rs948440

    upload_2020-7-30_18-59-9.png
    It can be seen that for variant ID's that have matches there are no significant datapoints - nothing approaching a pv or p value of 10-8 that is usually used as a decision gate in this UK biobank GWAS study.

    Sorry @Michiel Tack for taking things of track.

    EDIT : Just a little rant about researchers. They like to fill their papers with big words and sound important with this and that correlation used, but sometimes they just forget to use common sense when evaluating and reporting the data.
     
    Last edited: Jul 31, 2020
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  14. sea

    sea Senior Member (Voting Rights)

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    Look up forward and reverse orientation for a better explanation than I can come up with.

    The snp database used to report snps in whatever orientation researchers reported them so it wasn’t consistent throughout. Some companies like 23andme reported all snps in forward orientation and the difference has been a source of confusion for many.

    Some time ago dbSNP changed to reporting all snps in forward orientation so papers written before that change may have differences to what you find now when you look up snps.

    760C8DB2-9740-4F8B-9563-245B2FAC2CC7.jpeg
    The red arrow points to the forward orientation for this snp, C
    The green arrow points to the reverse orientation, G

    36ED51BF-71BD-42C6-8619-CC80881E153F.jpeg

    I haven’t looked at the other things you wrote about yet.
     
  15. wigglethemouse

    wigglethemouse Senior Member (Voting Rights)

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    Thank you @sea . That's why I enjoy coming here as there is always something to learn from others :)
     
  16. sea

    sea Senior Member (Voting Rights)

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    To be fair they don’t expect people to pull a single line from their chart. When you look at the entire chart the chromosome is listed for the first snp on each relevant chromosome. All subsequent snps on the same chromosome are listed on subsequent lines without repeating the chromosome number.

    I haven’t looked in detail at the frequencies and p values. I don’t have the brain for that at the moment. I agree it does appear odd to have a rare snp appear at such a high frequency in patients. It seems at odds though with the way they described their methods where they said they only included snps with MAF of 5% or greater :thumbsdown:
     
  17. Michiel Tack

    Michiel Tack Senior Member (Voting Rights)

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    No problem, thanks for probing into these studies. We need more people like you who focus on dissecting biomedical ME/CFS research.

    More relevant studies:

    Tores-Harding et al. 2004. Family Medical History of Persons with Chronic Fatigue Syndrome https://www.tandfonline.com/doi/abs/10.1300/J092v12n04_03

    Underhill & O'Gorman 2006. Prevalence of Chronic Fatigue Syndrome and Chronic Fatigue Within Families of CFS Patients https://www.tandfonline.com/doi/abs/10.1300/J092v13n01_02

    That sounds interesting but it sounds like it was a study based on self-report. Do you know more @Simon M ?
     
    Last edited: Jul 31, 2020
  18. Simon M

    Simon M Senior Member (Voting Rights)

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    Responding to tag.



    I am afraid I am not able to look at this at the moment. However, there is a review paper in press that looks at these issues and might be available quite soon.
     
  19. MSEsperanza

    MSEsperanza Senior Member (Voting Rights)

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  20. spinoza577

    spinoza577 Senior Member (Voting Rights)

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    This is referred to in Underhill 2015 [ME/CFS]: An infectious disease, open access (an interesting article).

    Apart from some genetic influence referred to, the article focuses, as the title says, on transmission (spouses are mentioned as well).
     
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